The sensitivity of electron scattering to the redistribution of valence electrons in bonded materials has been recognized for many years by theorists and materials scientists. Such chemical bonding effects change the shielding of the nucleus in a way that can have a dramatic effect on scattering amplitudes at low scattering angles. In materials science the effect has been used to try to understand mechanical and electronic properties of materials. However, the effects have not been studied in depth in the context of protein structure study by electron crystallography. Since data is generally collected within a lower range of scattering angles than in materials science there is the possibility that strong effects could be observed. The resultant changes in diffraction amplitudes could mislead the process of refining an initial atomic model if they produce an R-factor that is larger than expected. We have shown in preliminary work that such effects can indeed contribute that such effects can indeed contribute substantially to the R-factor at low to medium resolution. Our aim in this work is to allow the incorporation of chemical bonding effects into the calculation of structure factors from an atomic model. We will calculate a library of chemical bonding perturbations for the amino acids that show significant bonding effects as well as for ionizable groups. These perturbations can then be incorporated into the atomic model when computing the structure factors. This would allow both better reliability in the convergence of refinement and more straight forward interpretation of details within the structure of the charge on ionizable groups, thus making more complete our understanding of structures determined by electron crystallography.